diff --git a/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines b/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines
deleted file mode 100644
index c1ebafec0159993aab2b1525f952e5b28e714776..0000000000000000000000000000000000000000
--- a/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines
+++ /dev/null
@@ -1,8 +0,0 @@
-borg1
-borg2
-borg3
-borg4
-borg5
-borg6
-borg7
-borg8
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
deleted file mode 100644
index ee03c904028a9b25f447b0cd74457e8a2439d6fb..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
+++ /dev/null
@@ -1,163 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- object blockMeshDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-convertToMeters 0.25e-9;
-
-vertices
-(
- (0 0 0) //0
- (15 0 0)
- (15 3 0)
- (0 3 0)
- (0 0 12)
- (15 0 12)
- (15 3 12)
- (0 3 12) //7
- (22 0 0)
- (22 3 0)
- (22 0 12)
- (22 3 12) //11
- (31 0 0)
- (31 3 0)
- (31 0 12)
- (31 3 12) //15
- (20 9 0)
- (17 9 0)
- (20 9 12)
- (17 9 12) //19
- (0 9 0)
- (0 9 12) //21
- (31 9 0)
- (31 9 12) //23
- (17 18 0)
- (0 18 0)
- (17 18 12)
- (0 18 12) //27
- (31 18 0)
- (20 18 0)
- (31 18 12)
- (20 18 12) //31
- (17 21 0)
- (0 21 0)
- (17 21 12)
- (0 21 12) //35
- (31 21 0)
- (20 21 0)
- (31 21 12)
- (20 21 12) //39
- (17 25 0)
- (0 25 0)
- (17 25 12)
- (0 25 12) // 43
- (31 25 0)
- (20 25 0)
- (31 25 12)
- (20 25 12) // 47
-);
-
-blocks
-(
- hex (0 1 2 3 4 5 6 7) bottomWall (15 3 6) simpleGrading (1 1 1) //1
- hex (1 8 9 2 5 10 11 6) bottomWall (3 3 6) simpleGrading (1 1 1) //2
- hex (2 9 16 17 6 11 18 19) bottomWall (3 6 6) simpleGrading (1 1 1) //3
- hex (8 12 13 9 10 14 15 11) bottomWall (9 3 6) simpleGrading (1 1 1) //4
- hex (3 2 17 20 7 6 19 21) liquid (15 6 6) simpleGrading (1 1 1) //5
- hex (20 17 24 25 21 19 26 27) liquid (15 9 6) simpleGrading (1 1 1) //6
- hex (25 24 32 33 27 26 34 35) liquid (15 3 6) simpleGrading (1 1 1) //6A
- hex (17 16 29 24 19 18 31 26) liquid (3 9 6) simpleGrading (1 1 1) //7
- hex (16 22 28 29 18 23 30 31) liquid (9 9 6) simpleGrading (1 1 1) //8
- hex (29 28 36 37 31 30 38 39) liquid (9 3 6) simpleGrading (1 1 1) //8A
- hex (9 13 22 16 11 15 23 18) liquid (9 6 6) simpleGrading (1 1 1) //9
- hex (33 32 40 41 35 34 42 43) topWall (15 3 6) simpleGrading (1 1 1) //10
- hex (32 37 45 40 34 39 47 42) topWall (3 3 6) simpleGrading (1 1 1) //11
- hex (24 29 37 32 26 31 39 34) topWall (3 3 6) simpleGrading (1 1 1) //12
- hex (37 36 44 45 39 38 46 47) topWall (9 3 6) simpleGrading (1 1 1) //13
-);
-
-patches
-(
- cyclic
- periodicX
- (
- (0 4 7 3)
- (3 7 21 20)
- (20 21 27 25)
- (25 27 35 33)
- (33 35 43 41)
- (12 13 15 14)
- (13 22 23 15)
- (22 28 30 23)
- (28 36 38 30)
- (36 44 46 38)
- )
-
- cyclic
- periodicZ
- (
- (0 3 2 1)
- (1 2 9 8)
- (8 9 13 12)
- (2 17 16 9)
- (2 3 20 17)
- (9 16 22 13)
- (17 20 25 24)
- (16 29 28 22)
- (16 17 24 29)
- (24 25 33 32)
- (28 29 37 36)
- (32 33 41 40)
- (36 37 45 44)
- (32 40 45 37)
- (24 32 37 29)
- (4 5 6 7)
- (5 10 11 6)
- (10 14 15 11)
- (6 11 18 19)
- (7 6 19 21)
- (11 15 23 18)
- (19 26 27 21)
- (18 23 30 31)
- (18 31 26 19)
- (26 34 35 27)
- (30 38 39 31)
- (34 42 43 35)
- (38 46 47 39)
- (34 39 47 42)
- (26 31 39 34)
- )
-
- wall
- outerBoundaryBottom
- (
- (0 1 5 4)
- (1 8 10 5)
- (8 12 14 10)
- )
-
- wall
- outerBoundaryTop
- (
- (40 41 43 42)
- (44 45 47 46)
- (40 42 47 45)
- )
-);
-
-mergePatchPairs
-(
-);
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution
deleted file mode 100644
index 46670343363af32a79fcf7bd788316556b9de7d7..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution
+++ /dev/null
@@ -1,46 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object fvSolution;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-solvers
-{
- p
- {
- solver PCG;
- preconditioner DIC;
- tolerance 1e-06;
- relTol 0;
- }
-
- U
- {
- solver PBiCG;
- preconditioner DILU;
- tolerance 1e-05;
- relTol 0;
- }
-}
-
-PISO
-{
- nCorrectors 2;
- nNonOrthogonalCorrectors 0;
- pRefCell 0;
- pRefValue 0;
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict
deleted file mode 100644
index 6bd9f1538e2c0723d9505442bdf2453015012738..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict
+++ /dev/null
@@ -1,64 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-bottomWall
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure FCC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies molecule;
- tethered yes;
- orientationAngles ( 30 0 0 );
-}
-
-liquid
-{
- massDensity 1100;
- temperature 250;
- velocityDistribution maxwellian;
- bulkVelocity ( 245 0 0 );
- id Ne;
- mass 3.350996347e-26;
- latticeStructure SC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 45 0 0 );
-}
-
-topWall
-{
- massDensity 1220;
- temperature 200;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure BCC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies corner;
- tethered yes;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict
deleted file mode 100644
index 56a7bbee713bf0a24860dad6ad2e592c9e17f464..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict
+++ /dev/null
@@ -1,104 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 2 ( Ne Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential maitlandSmith;
- rCut 1e-09;
- rMin 1.5e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 7.5;
- rm 3.756e-10;
- epsilon 1.990108438e-21;
- }
-
- energyScalingFunction doubleSigmoid;
- doubleSigmoidCoeffs
- {
- shift1 9e-10;
- scale1 -64771072;
- shift2 9.7e-10;
- scale2 -259084288;
- }
-
- writeTables yes;
- }
-
- Ar-Ne
- {
- pairPotential maitlandSmith;
- rCut 9e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 4;
- rm 3.48e-10;
- epsilon 8.765026657e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables yes;
- }
-
- Ne-Ne
- {
- pairPotential maitlandSmith;
- rCut 8e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 5;
- rm 3.0739e-10;
- epsilon 5.813260729e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables yes;
- }
-}
-
-tether
-{
- Ar
- {
- tetherPotential restrainedHarmonicSpring;
- restrainedHarmonicSpringCoeffs
- {
- springConstant 0.1;
- rR 1.2e-09;
- }
- }
-}
-
-external
-{
- gravity ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution
deleted file mode 100644
index 46670343363af32a79fcf7bd788316556b9de7d7..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution
+++ /dev/null
@@ -1,46 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object fvSolution;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-solvers
-{
- p
- {
- solver PCG;
- preconditioner DIC;
- tolerance 1e-06;
- relTol 0;
- }
-
- U
- {
- solver PBiCG;
- preconditioner DILU;
- tolerance 1e-05;
- relTol 0;
- }
-}
-
-PISO
-{
- nCorrectors 2;
- nNonOrthogonalCorrectors 0;
- pRefCell 0;
- pRefValue 0;
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict
deleted file mode 100644
index 937130f4ac3ba22f29b727686566f27b6adfa45a..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict
+++ /dev/null
@@ -1,64 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-sectionA
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-sectionB
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ne;
- mass 3.350917e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-sectionC
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict
deleted file mode 100644
index 0386a6994e0d9708901895788978e11f2d5bf453..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict
+++ /dev/null
@@ -1,86 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 1 ( Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential maitlandSmith;
- rCut 1e-09;
- rMin 1.5e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 7.5;
- rm 3.756e-10;
- epsilon 1.990108438e-21;
- }
-
- energyScalingFunction doubleSigmoid;
- doubleSigmoidCoeffs
- {
- shift1 9e-10;
- scale1 -64771072;
- shift2 9.7e-10;
- scale2 -259084288;
- }
-
- writeTables no;
- }
-
- Ar-Ne
- {
- pairPotential maitlandSmith;
- rCut 9e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 4;
- rm 3.48e-10;
- epsilon 8.765026657e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables no;
- }
-
- Ne-Ne
- {
- pairPotential maitlandSmith;
- rCut 8e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 5;
- rm 3.0739e-10;
- epsilon 5.813260729e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables no;
- }
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
index 00dd874d7638805cf31b2c56b01b659e0792e1c4..d8245cb12bceacb3316f8f922262a9e911b9b155 100755
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
@@ -3,9 +3,20 @@
# Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions
-cd periodicCube
- rm -rf 0
- rm -rf Ar-Ar
- rm -rf constant/idList
+cd periodicCubeArgon
+ rm -rf 0/*
+ rm -f Ar-Ar
+ rm -f electrostatic
+ rm -f constant/idList
+ rm -rf constant/polyMesh/sets
+ cleanCase
+cd ..
+
+cd periodicCubeWater
+ rm -rf 0/*
+ rm -f O-O
+ rm -f electrostatic
+ rm -f constant/idList
+ rm -rf constant/polyMesh/sets
cleanCase
cd ..
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
index 0c590da09a8c91a0815034deba71b3d4d681e762..0d8c6de9d1b4ecf76f0d6b46642adac9dd514c8c 100755
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
@@ -5,9 +5,14 @@
application="mdEquilibrationFoam"
-cd periodicCube
+# cd periodicCubeArgon
+# runApplication blockMesh
+# runApplication mdInitialise
+# runApplication $application
+# cd ..
+
+cd periodicCubeWater
runApplication blockMesh
- runApplication molConfig
+ runApplication mdInitialise
runApplication $application
-cd ..
-
+cd ..
\ No newline at end of file
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution
deleted file mode 100644
index 46670343363af32a79fcf7bd788316556b9de7d7..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution
+++ /dev/null
@@ -1,46 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object fvSolution;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-solvers
-{
- p
- {
- solver PCG;
- preconditioner DIC;
- tolerance 1e-06;
- relTol 0;
- }
-
- U
- {
- solver PBiCG;
- preconditioner DILU;
- tolerance 1e-05;
- relTol 0;
- }
-}
-
-PISO
-{
- nCorrectors 2;
- nNonOrthogonalCorrectors 0;
- pRefCell 0;
- pRefValue 0;
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict
deleted file mode 100644
index 6f48e375e8c3ba101230631096b6ecd6df24a156..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict
+++ /dev/null
@@ -1,34 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-liquid
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict
deleted file mode 100644
index 1abf7b0e569b0a3b4dd0530d9c9f3ec332d43f6c..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict
+++ /dev/null
@@ -1,65 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 1 ( Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential azizChen;
- rCut 1.2e-09;
- rMin 1.5e-10;
- dr 2e-14;
- azizChenCoeffs
- {
- epsilon 1.97742255e-21;
- rm 3.759e-10;
- A 9502720;
- alpha 16.345655;
- C6 1.0914254;
- C8 0.6002595;
- C10 0.3700113;
- D 1.4;
- gamma 2;
- }
-
- energyScalingFunction noScaling;
- writeTables yes;
- }
-}
-
-tether
-{
- Ar
- {
- tetherPotential restrainedHarmonicSpring;
- restrainedHarmonicSpringCoeffs
- {
- springConstant 0.0277;
- rR 1.2e-09;
- }
- }
-}
-
-external
-{
- gravity ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..567fce489ce0f0bd6805f2a72cb5001db238cbcd
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties
@@ -0,0 +1,36 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+Ar
+{
+ siteIds (Ar);
+ pairPotentialSiteIds (Ar);
+ siteReferencePositions
+ (
+ (0 0 0)
+ );
+ siteMasses
+ (
+ 6.63352033e-26
+ );
+ siteCharges
+ (
+ 0
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
similarity index 71%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
index 187c2c7784d60dda7a64455a321799191e21c95e..23a2ee9874ef09ad03276bbe470cc179802a227c 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
@@ -1,17 +1,25 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
+
FoamFile
{
- version 2.0;
- format ascii;
- class dictionary;
- object blockMeshDict;
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object blockMeshDict;
}
+
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
convertToMeters 2.462491658e-9;
@@ -61,4 +69,5 @@ mergePatchPairs
(
);
+
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
similarity index 90%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
index b3548de91cf4646aa6692d8e02914c5ed4755ff7..850c9baa1ec078697b17ec724c99578c6047e10d 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
similarity index 92%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
index f1052a4864fad271f58b2d6f62e0f3898d42c81d..76f7ed8a7ee4afac7f47fb4c97b4a42a01147053 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,7 +10,6 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no;
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..958e14c73370e57528f6fd38a15607b7ba3c2bcd
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict
@@ -0,0 +1,64 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 2;
+
+method simple;
+
+simpleCoeffs
+{
+ n (2 1 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (1 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ processorWeights
+ (
+ 1
+ 3
+ );
+}
+
+manualCoeffs
+{
+ dataFile "";
+}
+
+distributed no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
similarity index 91%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
index 2dd296045bbd9676b0bf078bc53d2dc5e4958365..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
@@ -11,11 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdEquilibrationDict;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-equilibrationTargetTemperature 300;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..e044b8378542974b38127b812d5a4e04aa9e2ac3
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict
@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+equilibrationTargetTemperature 300.0;
+
+// ************************************************************************* //
\ No newline at end of file
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..cb562f34a6c148531c9a243458edb24af24b5de7
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict
@@ -0,0 +1,44 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+ massDensity 1220;
+ temperature 300;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds (Ar);
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..190428f399ffe941ecd05be8492411c4497c5b6c
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict
@@ -0,0 +1,121 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+n| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( Ar );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither is an error)
+
+pair
+{
+ Ar-Ar
+ {
+ pairPotential maitlandSmith;
+ rCut 1.0e-9;
+ rMin 0.15e-9;
+ dr 5e-14;
+ maitlandSmithCoeffs
+ {
+ m 13.0;
+ gamma 7.5;
+ rm 0.3756e-9;
+ epsilon 1.990108438e-21;
+ }
+ energyScalingFunction doubleSigmoid;
+ doubleSigmoidCoeffs
+ {
+ shift1 0.9e-9;
+ scale1 0.3e11;
+ shift2 0.97e-9;
+ scale2 1.2e11;
+ }
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..2486f3c146ba4495cb003f1912db45ff57b5aa55
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties
@@ -0,0 +1,72 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+ siteIds (H H O M);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+water2
+{
+ siteIds (H2 H2 O M2);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..b78ecf45c974246d6545e6265c8e459946d467bf
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
@@ -0,0 +1,73 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 2.10840e-9;
+
+vertices
+(
+ (-1 -1 -1)
+ (1 -1 -1)
+ (1 1 -1)
+ (-1 1 -1)
+ (-1 -1 1)
+ (1 -1 1)
+ (1 1 1)
+ (-1 1 1)
+);
+
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) liquid (12 12 11) simpleGrading (1 1 1)
+);
+
+patches
+(
+ cyclic
+ periodicX
+ (
+ (1 2 6 5)
+ (0 4 7 3)
+ )
+
+ cyclic
+ periodicY
+ (
+ (2 3 7 6)
+ (0 1 5 4)
+ )
+
+ cyclic
+ periodicZ
+ (
+ (0 3 2 1)
+ (4 5 6 7)
+ )
+)
+
+mergePatchPairs
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
similarity index 67%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
index e9d933420b7298f5aa2fef9909433f031b113f5a..27cc5e87df98bf4826a1a86391e91fbf982a59f1 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -15,33 +15,28 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-4
+3
(
periodicX
{
type cyclic;
- nFaces 288;
- startFace 10710;
+ nFaces 264;
+ startFace 4344;
featureCos 0.9;
}
- periodicZ
+ periodicY
{
type cyclic;
- nFaces 1296;
- startFace 10998;
+ nFaces 264;
+ startFace 4608;
featureCos 0.9;
}
- outerBoundaryBottom
- {
- type wall;
- nFaces 162;
- startFace 12294;
- }
- outerBoundaryTop
+ periodicZ
{
- type wall;
- nFaces 162;
- startFace 12456;
+ type cyclic;
+ nFaces 288;
+ startFace 4872;
+ featureCos 0.9;
}
)
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
similarity index 86%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
index 46436871638186b4ead04e658ceeadd2579b9a5f..51a42ecc0e828d90fd725f5c361eae36c95f5f15 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,7 +10,6 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -21,13 +20,13 @@ startTime 0;
stopAt endTime;
-endTime 3e-11;
+endTime 5e-12;
-deltaT 1e-14;
+deltaT 1e-15;
writeControl runTime;
-writeInterval 1e-12;
+writeInterval 2e-13;
purgeWrite 0;
@@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no;
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
similarity index 57%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
index 2b1855ea4634bda4d66c8129ce2d08d57a2fb0c9..e0302aafcc9b69d045a7b00b3a4a108a44973291 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
@@ -1,40 +1,52 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
+
FoamFile
{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object decomposeParDict;
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
}
+
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
numberOfSubdomains 4;
-method metis;
+method simple;
simpleCoeffs
{
- n ( 4 1 1 );
+ n (2 2 1);
delta 0.001;
}
hierarchicalCoeffs
{
- n ( 1 1 1 );
+ n (1 1 1);
delta 0.001;
order xyz;
}
metisCoeffs
{
- processorWeights ( 1 1 1 1 );
+ processorWeights
+ (
+ 1
+ 3
+ );
}
manualCoeffs
@@ -44,7 +56,9 @@ manualCoeffs
distributed no;
-roots ( );
+roots
+(
+);
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
similarity index 89%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
index dfef948901fc9407d740d27c3f58e12fc09f78c8..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
@@ -11,13 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdSolution;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
similarity index 79%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
index dfef948901fc9407d740d27c3f58e12fc09f78c8..de8cb745e1f62f9f76556059a8d34a750d5b808f 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,14 +10,10 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
- object mdSolution;
+ object mdEquilibrationDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
+targetTemperature 298;
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..ff1444ead5acf93663635513847686618cb704e5
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict
@@ -0,0 +1,53 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ water2
+ water
+ water2
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ (0 0.5 0.5)
+ (0.5 0 0.5)
+ (0.5 0.5 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..25b268e74c7e3e102b49eeaa23186dc47031e338
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict
@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( water );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If a pair are not present here it is assumed that they do not interact.
+
+// Electrostatic pair interactions are not listed here - they are handled
+// separately.
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither will throw an error)
+
+pair
+{
+ O-O
+ {
+ pairPotential lennardJones;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 1e-13;
+ lennardJonesCoeffs
+ {
+ sigma 3.154e-10;
+ epsilon 1.07690722e-21;
+ }
+ energyScalingFunction noScaling;
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1e-9;
+ rMin 2e-11;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
similarity index 57%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
index 11f901ce8e07f87b4c4e41b1be30311c5ecd5589..7ff7776cb12c793a7bed32339e31b6ded3897549 100755
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
@@ -3,14 +3,8 @@
# Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions
-cd constrictedChannel
- rm -rf 0
- rm -rf Ar-Ar Ar-Ne Ne-Ne
- rm -rf constant/idList
- cleanCase
-cd ..
-
cd nanoNozzle
+ rm -rf constant/polyMesh/sets
rm -rf processor[0-9]
cleanCase
cd ..
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
similarity index 60%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
index 640ecd9bdc14899a37fe41bf908956b6623fa5f3..c756b2ca7e7a3d0ac97842edb011c9f6891abc98 100755
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
@@ -3,13 +3,7 @@
# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions
-application="gnemdFoam"
-
-cd constrictedChannel
- runApplication blockMesh
- runApplication molConfig
- runApplication $application
-cd ..
+application="mdFoam"
cd nanoNozzle
runApplication blockMesh
@@ -17,7 +11,7 @@ cd nanoNozzle
runApplication decomposePar
hostname > system/machines
- runParallel molConfig 4 system/machines
+ runParallel mdInitialise 4 system/machines
runParallel $application 4 system/machines
runApplication reconstructPar
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..faf53865886ddd2133a0f6ad01f43d111d94c951
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties
@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+ siteIds (H H O M);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
similarity index 65%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
index 024f66a3838c1a7bd2348707c3fca7e080686015..bfd56736e27cc02fb354b8ce9de41ef67748dd03 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
@@ -14,9 +14,9 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-convertToMeters 3e-9;
+convertToMeters 3.2e-9;
-vertices
+vertices
(
(0 0 0)
(3.5 0 0)
@@ -44,47 +44,19 @@ vertices
(16 2.5 3.5)
);
-blocks
+blocks
(
- hex (0 1 2 3 4 5 6 7) sectionA (16 15 15) simpleGrading (1 1 1)
- hex (1 8 9 2 5 10 11 6) sectionA (16 15 15) simpleGrading (0.4 1 1)
- hex (8 12 13 9 10 14 15 11) sectionB (16 15 15) simpleGrading (1 1 1)
- hex (12 16 17 13 14 18 19 15) sectionC (11 15 15) simpleGrading (2.8 1 1)
- hex (16 20 21 17 18 22 23 19) sectionC (16 15 15) simpleGrading (1 1 1)
+ hex (0 1 2 3 4 5 6 7) sectionA (20 16 16) simpleGrading (1 1 1)
+ hex (1 8 9 2 5 10 11 6) sectionA (20 16 16) simpleGrading (1 1 1)
+ hex (8 12 13 9 10 14 15 11) sectionB (29 16 16) simpleGrading (1 1 1)
+ hex (12 16 17 13 14 18 19 15) sectionC (17 16 16) simpleGrading (1 1 1)
+ hex (16 20 21 17 18 22 23 19) sectionC (20 16 16) simpleGrading (1 1 1)
);
-edges
-(
- simpleSpline 12 16
- (
- (10.375 0.875 0.4)
- (10.75 0.75 0)
- (11.125 0.625 -0.4)
- )
-
- simpleSpline 14 18
- (
- (10.375 0.875 2.6)
- (10.75 0.75 3)
- (11.125 0.625 3.4)
- )
-
- simpleSpline 15 19
- (
- (10.375 2.125 2.6)
- (10.75 2.25 3)
- (11.125 2.375 3.4)
- )
-
- simpleSpline 13 17
- (
- (10.375 2.125 0.4)
- (10.75 2.25 0)
- (11.125 2.375 -0.4)
- )
-);
+edges
+();
-patches
+patches
(
patch
sectionAEnd
@@ -92,12 +64,12 @@ patches
(0 4 7 3)
)
- patch
+ wall
sectionCEnd
(
(20 21 23 22)
)
-
+
wall
front
(
@@ -107,7 +79,7 @@ patches
(12 16 18 14)
(16 20 22 18)
)
-
+
wall
back
(
@@ -117,7 +89,7 @@ patches
(13 15 19 17)
(17 19 23 21)
)
-
+
wall
top
(
@@ -127,7 +99,7 @@ patches
(14 18 19 15)
(18 22 23 19)
)
-
+
wall
bottom
(
@@ -139,7 +111,7 @@ patches
)
);
-mergePatchPairs
+mergePatchPairs
(
);
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
similarity index 66%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
index a58d17ed7f51a0b1d98167dadad04ec7b6a21c8b..8f1b5f6505e47c52d85bd170a7fae0d85f55ec1c 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -20,38 +20,38 @@ FoamFile
sectionAEnd
{
type patch;
- nFaces 225;
- startFace 48150;
+ nFaces 256;
+ startFace 77760;
}
sectionCEnd
{
- type patch;
- nFaces 225;
- startFace 48375;
+ type wall;
+ nFaces 256;
+ startFace 78016;
}
front
{
type wall;
- nFaces 1125;
- startFace 48600;
+ nFaces 1696;
+ startFace 78272;
}
back
{
type wall;
- nFaces 1125;
- startFace 49725;
+ nFaces 1696;
+ startFace 79968;
}
top
{
type wall;
- nFaces 1125;
- startFace 50850;
+ nFaces 1696;
+ startFace 81664;
}
bottom
{
type wall;
- nFaces 1125;
- startFace 51975;
+ nFaces 1696;
+ startFace 83360;
}
)
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
similarity index 86%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
index c43b52a4489940816c201cd8c03c5ca1f7694a2e..8a3ba006163857eb4fafe09388c1ae873b0f23bf 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,7 +10,6 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -21,13 +20,13 @@ startTime 0;
stopAt endTime;
-endTime 8e-11;
+endTime 1e-10;
-deltaT 1e-14;
+deltaT 1e-15;
writeControl runTime;
-writeInterval 2e-12;
+writeInterval 2e-13;
purgeWrite 0;
@@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no;
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..a3946a745f2169cea62449bd32b9365bd539cd69
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict
@@ -0,0 +1,66 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method metis;
+
+simpleCoeffs
+{
+ n (2 2 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (1 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ processorWeights
+ (
+ 1
+ 1
+ 1
+ 1
+ );
+}
+
+manualCoeffs
+{
+ dataFile "";
+}
+
+distributed no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
similarity index 89%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
index dfef948901fc9407d740d27c3f58e12fc09f78c8..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
@@ -11,13 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdSolution;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..de8cb745e1f62f9f76556059a8d34a750d5b808f
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict
@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature 298;
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..ac85160f5cb2e1cbc774f42df6b87eb70ccd320d
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict
@@ -0,0 +1,85 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+sectionA
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionB
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionC
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..25b268e74c7e3e102b49eeaa23186dc47031e338
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict
@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( water );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If a pair are not present here it is assumed that they do not interact.
+
+// Electrostatic pair interactions are not listed here - they are handled
+// separately.
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither will throw an error)
+
+pair
+{
+ O-O
+ {
+ pairPotential lennardJones;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 1e-13;
+ lennardJonesCoeffs
+ {
+ sigma 3.154e-10;
+ epsilon 1.07690722e-21;
+ }
+ energyScalingFunction noScaling;
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1e-9;
+ rMin 2e-11;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines b/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines
deleted file mode 100644
index 4b24efafd5ca1ad451a6018d16f638079b1a4f8b..0000000000000000000000000000000000000000
--- a/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines
+++ /dev/null
@@ -1 +0,0 @@
-noisy